I just got through with the second file. I had gotten up to the Elite Four before I stopped in the first. However, when I beat the Elite 4 in this second file and started the game again, the data had been erased. I didn't make any save states after I first confirmed my SID while in Birch's lab, so I have to start all over :/
It's not so bad, since it only took me 3-4 hours to play through it, but I would like to know what I did. The Emerald file had been displaying the "Save data was corrupted. Starting from previous save" line for a while, but when I Ctrl-R'd after the Elite 4, the first time I'd done so since I made that savestate in the lab, it said the whole file was corrupted. What did I do that could have caused this?